Hi Doug,
I was on mscoc2.
I am working from /usr/people/ED/s1407886/big_run/vina and command I ran was ~douglas/scripts/docking/autoAD.ksh -cqpjv top10k.sdf protein.pdb sites.mol2 as per the tutorial.
It ran fine as I listed the .dlg files and could see them being made, however, it was just very slow. I kept running it overnight but the VPN connection was eventually lost and so I can't send a screen shot.
How long should I expect these runs to take?